Output format options

Five output formats are offered. You can choose more than one (or all 5 if you wish).

CLUSTAL format output is a self explanatory alignment format. It shows the sequences aligned in blocks. It can be read in again at a later date to (for example) calculate a phylogenetic tree or add a new sequence with a profile alignment.

GCG output can be used by any of the GCG or EGCG programs that can work on multiple alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG .msf format files (multiple sequence file); new in version 7 of GCG.

PHYLIP format output can be used for input to the PHYLIP package of Joe Felsenstein. This is an extremely widely used package for doing every imaginable form of phylogenetic analysis (MUCH more than the the modest intro- duction offered by this program).

NBRF/PIR: this is the same as the standard PIR format with ONE ADDITION. Gap characters "-" are used to indicate the positions of gaps in the multiple alignment. These files can be re-used as input in any part of clustal that allows sequences (or alignments or profiles) to be read in.

GDE: this format is used by the GDE package of Steven Smith.

GDE OUTPUT CASE: sequences in GDE format may be written in either upper or lower case.

CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the alignment lines in clustalw format.

OUTPUT ORDER is used to control the order of the sequences in the output alignments. By default, the order corresponds to the order in which the sequences were aligned (from the guide tree/dendrogram), thus automatically grouping closely related sequences. This switch can be used to set the order to the same as the input file.

PARAMETER OUTPUT: This option allows you to save all your parameter settings in a parameter file. This file can be used subsequently to rerun ClustalW using the same parameters.